We humans are part of the web of life in a way that is somewhat unpleasant to consider. We think of parasites as those things that grow on trees and use the tree's sap for fuel, like mistletoe. We know about the parasites that you can get in your gut from traveling. But we don't like to think about the millions of microbes that live in our guts, on our skin, in our noses, and unfortunately, inside every cell in our bodies. In fact, at least of quarter of us have Staphylococcus aureus living inside our noses. This is the microbe that is called MRSA when it has become resistant to the antibiotic methycillin.

Sometimes the things that live on and in us are actually useful. At that point it is no longer a parasitic relationship, it is more of a synbiosis or eubiosis. There are bugs (microbes) in our guts that help digest our food, and also that make vitamins that we need. Mitochondria are organelles inside our cells that were probably parasites at one time, but they were so useful that we came to depend on them. They make ATP, the cash of energy currency in the body. We know that mitochondria were most likely independent organisms because they have their own DNA.

Relatively recently in human history, a bold man drank a potion of Helicobacter pylori bacteria, and gave himself gastric ulcers. Before that we didn't know that particular bug had much to do with ulcer formation. But now we know. And most of us have at least a few of this bug in us. In fact, pretty much all of us have a few of lots of different kinds of bugs that could be dangerous if they overgrew.

We get some microbes from our parents, and gain new ones throughout life. Babies who are born the normal way, through their mother's vagina, get their mother's vaginal flora in their mouths and swallow it. That sets up the kind of biota that lives in their guts for life. Usually a child's gut biota is fairly stable by age 3. A lot of our gut biota depends on what we eat. A sugary diet sets up a whole different community than a vegetable and fiber-rich diet. You can guess at which one is better for you. A stable community in your gut is protective because it stops other kinds from getting established. People with very stable healthy populations of bugs in their guts can eat anything and never get sick from it.

Stomach acid is the other normal way that we prevent new or bad bugs from setting up house inside us. Infants don't have much acid, so they are especially susceptible to whatever they eat. Adults normally have such strong acid that not much survives the stomach and gets to the intestines. But if we block our stomach acid with anti-acids, we are at risk for getting the wrong kinds of bugs in our guts.

The fastest way to mess up your microbial communities is to take antibiotics. The more high powered the drugs, the more imbalanced your biota will be as a result. The more often you take antibiotics, the more the remaining community will be antibiotic resistant. The bug that really hits hard on people who've taken a lot of antibiotics is called Clostridium difficile. It is on the CDC's list of extremely dangerous antibiotic resistant bugs.

In naturopathic-speak we call your body the "terrain". It is the ground upon which things grow. The list of possible infections is endless, and the number of bugs on and in you this very moment is also endless. As long as we are strong and relaxed and young enough, we don't get sick. When we get run down and weak the microbes can get the better of us. Stress from life events raises our cortisol and decreases our immune response, and the microbial populations start booming. We feed them sugary junk, and don't exercise enough, and don't keep our bowel movements regular, and they start running the show. It is possible to end up sick from the same bugs that you've been carrying around for 40 years or more.

There's new research that shows that depression, anxiety, and obesity are linked to particular sets of gut bugs. Experiments in mice and humans have shown that taking the microbes from an anxious person's gut and putting them in a calm person will make change what we thought was their personality. And switching gut bugs in mice can make a fat mouse skinny and vice versa. The wrong gut bugs are linked to all kinds of diseases of the gut, from ulcerative colitis and crohn's disease to IBS. There's a lot more information coming down the pipe about this. Supplement companies are trying to figure out how to introduce the right microbes into people's guts to help them heal from various diseases and mental states.

There's not much you can do about the fact that you will be exposed to microbes. No amount of antibacterial soap will protect you. The thing that will is keeping yourself healthy and calm enough to mount a good immune response. That way you keep the populations down to reasonable levels, where they may even help you somehow. Oh, and garlic will help. Garlic turns out to be the very simplest way to keep your gut biota in line. If you can stand it, some raw garlic every day kills the baddies and keeps the goodies. If you can't stand it, you might need some more advanced help.